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fix: max_v flag initial value#30

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stanfish06 wants to merge 2 commits intojmbreda:masterfrom
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Open

fix: max_v flag initial value#30
stanfish06 wants to merge 2 commits intojmbreda:masterfrom
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@stanfish06 stanfish06 commented Feb 6, 2026

Fix #28

After changing the initial value of max_v_str to false, running Sanity with default parameters produced log_transcription_quotients.txt not log_transcription_quotients_vmax.txt.

Here is a verification:

stanfish@StanFishDeb:~/tmp/Sanity$ git diff
diff --git a/src/calc_true_variation_parallel_prior_mu_sigma.cpp b/src/calc_true_variation_parallel_prior_mu_sigma.cpp
index 8975d08..156548d 100644
--- a/src/calc_true_variation_parallel_prior_mu_sigma.cpp
+++ b/src/calc_true_variation_parallel_prior_mu_sigma.cpp
@@ -755,7 +755,7 @@ void parse_argv(int argc,char** argv, string &in_file, string &gene_name_file, s
        int N_param(11);
        string extended_output("false");
        string no_norm_str("false");
-       string max_v_str("true");
+       string max_v_str("false");
     string to_find[11][2] = {{"-f", "--file"},
                                                        {"-d", "--destination"},
                                                        {"-n", "--n_threads"},
stanfish@StanFishDeb:~/tmp/Sanity$ cd src/ && make
g++ -I. -O2 -ffast-math -O3 -fopenmp -std=c++11 -o ../bin/Sanity calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
stanfish@StanFishDeb:~/tmp/Sanity/src$ cd ..
stanfish@StanFishDeb:~/tmp/Sanity$ cd bin/
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2252
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  6 11:54 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  6 11:47 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  6 11:47 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  6 11:47 Sanity_macOS
stanfish@StanFishDeb:~/tmp/Sanity/bin$ cat > matrix.csv <<'EOF'
1,2,3
4,5,6
7,8,9
10,11,12
EOF
stanfish@StanFishDeb:~/tmp/Sanity/bin$ cat matrix.csv
1,2,3
4,5,6
7,8,9
10,11,12
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ./Sanity -f matrix.csv
File type : csv
There were 3 rows
There were 3 genes and 2 cells
Estimated memory usage: 33 KB
Fit gene expression levels
First process now fitting gene 0 out of 0.
Print output
stanfish@StanFishDeb:~/tmp/Sanity/bin$ ls -l
total 2264
-rw-rw-r-- 1 stanfish stanfish      73 Feb  6 11:54 log_transcription_quotients.txt
-rw-rw-r-- 1 stanfish stanfish      65 Feb  6 11:54 ltq_error_bars.txt
-rw-rw-r-- 1 stanfish stanfish      27 Feb  6 11:54 matrix.csv
-rwxrwxr-x 1 stanfish stanfish   98608 Feb  6 11:54 Sanity
-rwxrwxr-x 1 stanfish stanfish   45800 Feb  6 11:47 Sanity_distance
-rwxrwxr-x 1 stanfish stanfish   45608 Feb  6 11:47 Sanity_gene_correlation
-rwxrwxr-x 1 stanfish stanfish 2103884 Feb  6 11:47 Sanity_macOS

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BUG: default parameters output log_transcription_quotients_vmax.txt instead of log_transcription_quotients.txt

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